Commits for vsmalladi

v249_preview to v249_preview2 (2011-03-15 to 2011-03-22) v249

• Removed 2 experiments K562 NF-YA and NF-YB the were submitted using incorrect lanes.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 231, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 20, context: html, text, full: html, text
• Removed 2 experiments as they used the wrong lanes (K562: NF-YA and NF-YB). Advised by lab to revoke data from hg18.
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra - lines changed 3730, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.new.ra - lines changed 2349, context: html, text, full: html, text
• Added track description as provided by Peggy Farnham.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.html - lines changed 90, context: html, text, full: html, text
• Removed specificiation of human protocols in protocols link.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.html - lines changed 1, context: html, text, full: html, text
• Added 1 submission, subId 3811.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrTfbs.ra - lines changed 157, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrTfbs.ra - lines changed 20, context: html, text, full: html, text
• Added 1 submission, subId 3812.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeLicrHistone.ra - lines changed 157, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeLicrHistone.ra - lines changed 20, context: html, text, full: html, text
• Updated DAF settings. Alignments will be download only. Lab will be submitting csfasta and csqual files instead of fastqs. Updated long label for Signal to say Signal instead of Peaks.
  • src/hg/encode/DAFs/2.0/stanfordNucleosome.daf - lines changed 12, context: html, text, full: html, text
• Merge branch 'master' into Development
• Undid load of 3 submissions due to meta-data errors: 3752,3751,3749.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 1256, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra - lines changed 334, context: html, text, full: html, text
• Removed 12 files and meta-data as advised by lab. Redmine issue 3057 note 6.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 283, context: html, text, full: html, text
• Added submission 3755.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 129, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 21, context: html, text, full: html, text
• First pass of SYDH Mouse RNA-seq DAF.
  • src/hg/encode/DAFs/2.0/stanfordMm9RnaSeq.daf - lines changed 60, context: html, text, full: html, text
• Added replicates required at Peak level. Need to confirm with lab if this is correct.
  • src/hg/encode/DAFs/2.0/stanfordMm9RnaSeq.daf - lines changed 1, context: html, text, full: html, text
• Added 7 new submissions mouse data.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra - lines changed 1059, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.newR2.ra - lines changed 127, context: html, text, full: html, text
• Reloaded data with normal table and file naming schema, removed docId naming strategy. Also removed fastq files, as these are not the correct RawData format that will be provided by the lab.
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSydhNsome.ra - lines changed 617, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhNsome.ra - lines changed 27, context: html, text, full: html, text
• Updated wgEncodeSydhNsome to use global tag's rather than local tags.
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
• Renamed 7 replicates as provided by Lab. Redmine issue: 2985.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 120, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra - lines changed 85, context: html, text, full: html, text
• Updated UW display with initial attic design for supplemental experiments.
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeUwDnase.ra - lines changed 51, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/wgEncodeUwDnase.ra - lines changed 287, context: html, text, full: html, text
• Added release notes to new html file and removed meta-data of replaced files.
  • src/hg/makeDb/trackDb/human/hg18/metaDb/alpha/wgEncodeYaleChIPseq.ra - lines changed 460, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.new.html - lines changed 178, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleChIPseq.new.ra - lines changed 1, context: html, text, full: html, text
• Fixed missing underscore(_) in GATA2SC267=GATA2(SC-267)
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra - lines changed 1, context: html, text, full: html, text
• Release notes of release 4 of track.
  • src/hg/makeDb/doc/encodeDccHg18/wgEncodeYaleChIPseq.release4.notes.txt - lines changed 1466, context: html, text, full: html, text
• Updated release notes to have path for files.
  • src/hg/makeDb/doc/encodeDccHg18/wgEncodeYaleChIPseq.release4.notes.txt - lines changed 1110, context: html, text, full: html, text
• Removed accession number for wgEncodeUwAffyExonArray track. Accession number has been migrated to metaDb as var=dccInternalNotes. Redmine issue 1492 note 17.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra - lines changed 1, context: html, text, full: html, text
• Added strain and age information for know Mouse cell lines.
  • src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 18, context: html, text, full: html, text
• Accidently checked in some changes I was playing with. Restoring commig 4888a0b7264461d213f0e0970d4a9fd9b074d983.
  • src/hg/encode/encodeLoad/doEncodeUnload.pl - lines changed 3, context: html, text, full: html, text
• Updated default tracks on to be all cell lines and Histone marks. Updated default signal windowing function to be mean+whiskers.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra - lines changed 5, context: html, text, full: html, text
• Updated spacing of trackDb enteries.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra - lines changed 4, context: html, text, full: html, text
• Updated spacing and removed some extra comment lines.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.ra - lines changed 8, context: html, text, full: html, text